DESCRIPTION

NAME kissnp, version DiscoSnp - kissnp submodule 1.2.5 - Copyright INRIA - CeCILL License

SYNOPSIS kissnp2/kissnp2 <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] -o name [-t] [-e length] [-l] [-b] [-k value] [-c value] [-g value] [-h]

  • or:

kissnp2/kissnp2 input_names_file.txt -o name [-t] [-e length] [-l] [-b] [-k value] [-c value] [-g value] [-h]

  • with "input_names_file.txt" being a file containing on each line the name of read files

DESCRIPTION

  • "kissnp2", detects SNPs from read set(s). It should usually be followed by the "kissreads" for recovering coverage and quality information from reads.

MANDATORY

  • At least one read set. -o file_name_prefix: where to write outputs and debruijn graph structure files.

OPTIONS -t extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with -T -T extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with -t -e length: extend found SNPs (option -t) and conserve only those whose min(left and right extension) is bigger or equal to "length" -l conserve low complexity SNPs. Default: false (filter out low complexity results) -b INT:

0: forbid SNPs for wich any of the two paths is branching (high precision, low recall).

Default value

  • 1: forbid SNPs for wich the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position 2: No limitation on branching (low precision, high recall) -k size_seed: will use seeds of length size_seed. Default: 27. -c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2 -C max_coverage: a sequence is covered by at most max_coverage coherent reads. Default: infiny (=2147483647 on your computer :) ) -g estimated_genome_size: estimation of the size of the genome whose reads come from.

  • It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion -h prints this message and exit

DiscoSnp - kissnp submodule 1.2.5 - Copyright INRIA - CeCILL License The command line was: kissnp2/kissnp2 -h

RELATED TO kissnp2…

The full documentation for kissnp2 is maintained as a Texinfo manual. If the info and kissnp2 programs are properly installed at your site, the command

  • info kissnp2

should give you access to the complete manual.